Merge branch 'main' into feature/runlist_configs

# Conflicts:
#	pyV2DL3/vegas/fillEVENTS_not_safe.py

.gitattributes

@@ -1 +1 @@
-*.ipynb filter=nbstrip_full
+*.ipynb filter=nbstrip_full

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
+

.github/workflows/pypi.yml

@@ -10,13 +10,13 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # make sure we have version info
       - run: git fetch --tags
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.9"
 

.github/workflows/v2dl3-codeChecking.yml

@@ -22,12 +22,12 @@ jobs:
         python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/v2dl3-eventdisplay-packaging.yml

@@ -62,7 +62,7 @@ jobs:
           flavor: latest=true
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           build-args: BUILD_BRANCH=${{ env.BUILD_BRANCH }}

.github/workflows/v2dl3-eventdisplay.yml

@@ -22,26 +22,21 @@ jobs:
         python-version: ["3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install mamba
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: environment-eventdisplay.yml
-          create-args: python=${{ matrix.python-version }}
-          init-shell: bash
+      - name: Pip install
+        run: |
+          pip install .[tests]
 
       - name: pytest
         shell: bash -leo pipefail {0}
-        env:
-          PYTHONPATH: .
         run: |
           pytest .
 
@@ -51,16 +46,14 @@ jobs:
 
       - name: Eventdisplay-pointlike
         shell: bash -leo pipefail {0}
-        env:
-          PYTHONPATH: .
         run: |
           # point-like tests
-          python pyV2DL3/script/v2dl3_for_Eventdisplay.py \
+          v2dl3-eventdisplay \
                -f ./64080.anasum.root \
                   ./effectiveArea.root \
                   --logfile test-pointlike.fits.log \
                   test-pointlike-CI.fits.gz
-          python pyV2DL3/script/compareFitsFiles.py \
+          v2dl3-compareFitsFiles \
                 -f ED-pointlike-CI.fits.gz test-pointlike-CI.fits.gz \
                 -d test-pointlike.log
           cat test-pointlike.log
@@ -72,12 +65,12 @@ jobs:
           PYTHONPATH: .
         run: |
           # full-enclosure tests
-          python pyV2DL3/script/v2dl3_for_Eventdisplay.py --full-enclosure \
+          v2dl3-eventdisplay --full-enclosure \
                -f ./64080.anasum.root \
                   ./effectiveArea.root \
                   --logfile test-full-enclosure.fits.log \
                   test-full-enclosure-CI.fits.gz
-          python pyV2DL3/script/compareFitsFiles.py \
+          v2dl3-compareFitsFiles \
                 -f ED-fullenclosure-CI.fits.gz test-full-enclosure-CI.fits.gz \
                 -d test-full-enclosure.log
           cat test-full-enclosure.log
@@ -89,13 +82,13 @@ jobs:
           PYTHONPATH: .
         run: |
           # point-like tests (with DB)
-          python pyV2DL3/script/v2dl3_for_Eventdisplay.py \
+          v2dl3-eventdisplay \
                -f ./64080.anasum.root \
                   ./effectiveArea.root \
                   --db_fits_file ./64080.db.fits.gz \
                   --logfile test-pointlike-db.fits.log \
                   test-pointlike-db-CI.fits.gz
-          python pyV2DL3/script/compareFitsFiles.py \
+          v2dl3-compareFitsFiles \
                 -f ED-pointlike-db-CI.fits.gz test-pointlike-db-CI.fits.gz \
                 -d test-pointlike-db.log
           cat test-pointlike-db.log
@@ -107,13 +100,13 @@ jobs:
           PYTHONPATH: .
         run: |
           # point-like tests with event selection
-          python pyV2DL3/script/v2dl3_for_Eventdisplay.py \
+          v2dl3-eventdisplay \
                -f ./64080.allevents.anasum.root \
                   ./effectiveArea.root \
                   --evt_filter eventfilter.yml \
                   --logfile test-pointlike-all.fits.log \
                   test-pointlike-all-CI.fits.gz
-          python pyV2DL3/script/compareFitsFiles.py \
+          v2dl3-compareFitsFiles \
                 -f ED-pointlike-all-CI.fits.gz test-pointlike-all-CI.fits.gz \
                 -d test-pointlike-all.log
           cat test-pointlike-all.log
@@ -125,13 +118,13 @@ jobs:
           PYTHONPATH: .
         run: |
           # full-enclosure tests with event selection
-          python pyV2DL3/script/v2dl3_for_Eventdisplay.py --full-enclosure \
+          v2dl3-eventdisplay --full-enclosure \
                -f ./64080.allevents.anasum.root \
                   ./effectiveArea.root \
                   --evt_filter eventfilter.yml \
                   --logfile test-full-enclosure-all.fits.log \
                   test-full-enclosure-all-CI.fits.gz
-          python pyV2DL3/script/compareFitsFiles.py \
+          v2dl3-compareFitsFiles \
                 -f ED-full-enclosure-all-CI.fits.gz test-full-enclosure-all-CI.fits.gz \
                 -d test-full-enclosure-all.log
           cat test-full-enclosure-all.log

.github/workflows/v2dl3-vegas.yml

@@ -34,7 +34,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout new branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Pull docker image
         run: |
@@ -55,7 +55,7 @@ jobs:
           sudo rm -rf $GITHUB_WORKSPACE/*
 
       - name: Checkout main branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: main
 

.pre-commit-config.yaml

@@ -1,19 +1,51 @@
 repos:
   # https://pycqa.github.io/isort/docs/configuration/black_compatibility.html#integration-with-pre-commit
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
   # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html?highlight=other%20tools#flake8
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
-        args: ["--max-line-length=100", "--extend-ignore=E203,E712"]
+        args: ["--max-line-length=125", "--extend-ignore=E203,E712"]
   # https://github.com/pre-commit/pre-commit-hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
+      - id: check-added-large-files
+        args: ['--maxkb=500']
+  # Github action
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.4
+    hooks:
+      - id: actionlint
+  # https://pyproject-fmt.readthedocs.io/en/latest/
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "v2.5.0"
+    hooks:
+      - id: pyproject-fmt
+  # codespell
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: [
+          "--ignore-words-list=livetime",
+        ]
+  # markdownlint
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.43.0
+    hooks:
+      - id: markdownlint
+        args: ["--disable", "MD041"]
+  # yamllint
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args: ["--strict", "-d", '{rules: {line-length: {max: 250}}}']

README_vegas.md

@@ -9,7 +9,7 @@ Events which fall outside the FoV defined in your EA file's cuts parameters will
 Use `-r 2` to choose ITM reconstruction instead of standard. If you're using a King PSF, make sure your parameters file is for the appropriate reconstruction type.
 
 ## Full Enclosure Analysis
-`--full-enclosure` 
+`--full-enclosure`
 
 v2dl3-vegas now supports full-enclosure via King PSF. Point-like remains default.
 

pyV2DL3/addHDUClassKeyword.py

@@ -1,6 +1,4 @@
-from pyV2DL3.constant import HDUCLASS
-from pyV2DL3.constant import HDUDOC
-from pyV2DL3.constant import HDUVERS
+from pyV2DL3.constant import HDUCLASS, HDUDOC, HDUVERS
 
 
 def addHDUClassKeyword(hdu, class1, class2=None, class3=None, class4=None):

pyV2DL3/eventdisplay/fillEVENTS.py

@@ -3,6 +3,7 @@
 import numpy as np
 import uproot
 from astropy.time import Time
+from scipy.stats import circmean
 
 from pyV2DL3.constant import (
     VTS_REFERENCE_HEIGHT,
@@ -17,7 +18,6 @@
     getRunQuality,
     produce_tel_list,
 )
-from scipy.stats import circmean
 
 logger = logging.getLogger(__name__)
 

pyV2DL3/genHDUList.py

@@ -28,7 +28,7 @@ def genPrimaryHDU():
 
 def loadROOTFiles(data_file, effective_area_file, file_type, **kwargs):
     """
-    Load event lists, event header, and instrument reponse functions
+    Load event lists, event header, and instrument response functions
     from VEGAS / Eventdisplay ROOT files.
 
     """

pyV2DL3/script/compareFitsFiles.py

@@ -2,8 +2,8 @@
 #
 # compare two fits files and write
 # differences into a file
-from astropy.io import fits
 import click
+from astropy.io import fits
 
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 

pyV2DL3/script/v2dl3_for_vegas.py

@@ -5,7 +5,6 @@
 
 from pyV2DL3.generateObsHduIndex import create_obs_hdu_index_file
 
-
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
 
@@ -161,11 +160,10 @@ def cli(
         print("Logging level INFO")
 
     logging.debug("Start importing ROOT")
-    from pyV2DL3.genHDUList import genHDUlist
-    from pyV2DL3.genHDUList import loadROOTFiles
-    from pyV2DL3.vegas.root_lib_util import (
+    from pyV2DL3.genHDUList import genHDUlist, loadROOTFiles
+    from pyV2DL3.vegas.root_lib_util import (  # Lundy- I don't like that this is where these are imported
         cpp_print_context,
-    )  # Lundy- I don't like that this is where these are imported
+    )
 
     # Store in a dict the IRFs to be stored within a file.
     # By default we will only store point-like IRFs.
@@ -380,10 +378,12 @@ def make_eclass_path(output, fname_base, eclass_idx):
 
 
 def runlist_to_file_pairs(runlist, event_class_mode, output):
-    from pyV2DL3.vegas.parseSt6RunList import parseRunlistStrs
-    from pyV2DL3.vegas.parseSt6RunList import RunlistParsingError
-    from pyV2DL3.vegas.parseSt6RunList import RunlistValidationError
-    from pyV2DL3.vegas.parseSt6RunList import validateRunlist
+    from pyV2DL3.vegas.parseSt6RunList import (
+        RunlistParsingError,
+        RunlistValidationError,
+        parseRunlistStrs,
+        validateRunlist,
+    )
 
     with open(runlist) as f:
         lines = f.readlines()

pyV2DL3/tests/test_IrfExtractor.py

@@ -1,6 +1,6 @@
 import numpy as np
-from pyV2DL3.eventdisplay.IrfExtractor import find_closest_az
-from pyV2DL3.eventdisplay.IrfExtractor import find_nearest
+
+from pyV2DL3.eventdisplay.IrfExtractor import find_closest_az, find_nearest
 
 
 def test_find_nearest():

pyV2DL3/tests/test_addHDUClassKeyword.py

@@ -1,5 +1,6 @@
-from astropy.io import fits
 import numpy as np
+from astropy.io import fits
+
 import pyV2DL3.addHDUClassKeyword
 
 

pyV2DL3/tests/test_util.py

@@ -1,7 +1,7 @@
-from pyV2DL3.eventdisplay.util import getGTI
-from pyV2DL3.eventdisplay.util import getRunQuality
 import numpy as np
 
+from pyV2DL3.eventdisplay.util import getGTI, getRunQuality
+
 
 def test_getRunQuality():
     vpm_messages = [

pyV2DL3/vegas/EffectiveAreaFile.py

@@ -1,10 +1,11 @@
-import ROOT
 import logging
-import numpy as np
 from ctypes import c_float
 
-from pyV2DL3.vegas.util import getCuts
+import numpy as np
+import ROOT
+
 from pyV2DL3.vegas.load_vegas import VEGASStatus
+from pyV2DL3.vegas.util import getCuts
 
 logger = logging.getLogger(__name__)